COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
Abstract
MOTIVATION: The boost of next-generation sequencing technologies provides us with an unprecedented opportunity for elucidating genetic mysteries, yet the short-read length hinders us from better assembling the genome from scratch. New protocols now exist that can generate overlapping pair-end reads. By joining the 3' ends of each read pair, one is able to construct longer reads for assembling. However, effectively joining two overlapped pair-end reads remains a challenging task. RESULT: In this article, we present an efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads. AVAILABILITY AND IMPLEMENTATION: COPE is implemented in C++ and is freely available as open-source code at ftp://ftp.genomics.org.cn/pub/cope. CONTACT: twlam@cs.hku.hk or luoruibang@genomics.org.cn
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COPE considers that k-mers that occur infrequently are likely to be sequencing errors.
“Thus, it considers that k-mers that occur infrequently are likely to be sequencing errors.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Liu et al., 2012
COPE is designed to handle deep genome sequencing datasets.
“COPE is designed to handle deep genome sequencing datasets.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Liu et al., 2012
COPE deploys an analogous approach as FLASH for finding the best overlap, but also takes into account the quality scores of mismatches.
“COPE deploys an analogous approach as FLASH for finding the best overlap, but also takes into account the quality scores of mismatches.”
From PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2014) · cites this paper as Liu et al., 2012
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- Authors
- Liu, B., Yuan, J., Yiu, S.-M., Li, Z., Xie, Y., Chen, Y., Shi, Y., Zhang, H., Li, Y., Lam, T.-W., & Luo, R.
- Affiliations
- University of Hong Kong (HK)
- Corresponding author
- Lam, Tak-Wah
- Luo, Ruibang
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-10-08
- Volume
- 28
- Issue
- 22
- Pages
- 2870-2874
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2103828958
- Cited by
- 138
- References
- 14
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 4 · 2023: 7 · 2022: 4 · 2021: 10 · 2020: 6 · 2019: 11 · 2018: 16 · 2017: 19 · 2016: 20 · 2015: 13 · 2014: 15 · 2013: 8
- FWCI
- 4.62
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- COPE, k-mer frequency, genome assembly, Arabidopsis thaliana
- MeSH terms
- Algorithms, Chromosome Mapping, Arabidopsis, Sequence Analysis, DNA, Contig Mapping, Genomics
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